mqScpData {scp} | R Documentation

## Example MaxQuant/SCoPE2 output

### Description

A `data.frame` with 1088 observations and 139 variables, as produced by reading a MaxQuant output file with `read.delim()`.

- Sequence: a character vector

- Length: a numeric vector

- Modifications: a character vector

- Modified.sequence: a character vector

- Deamidation..N..Probabilities: a character vector

- Oxidation..M..Probabilities: a character vector

- Deamidation..N..Score.Diffs: a character vector

- Oxidation..M..Score.Diffs: a character vector

- Acetyl..Protein.N.term.: a numeric vector

- Deamidation..N.: a numeric vector

- Oxidation..M.: a numeric vector

- Missed.cleavages: a numeric vector

- Proteins: a character vector

- Leading.proteins: a character vector

- protein: a character vector

- Gene.names: a character vector

- Protein.names: a character vector

- Type: a character vector

- Set: a character vector

- MS.MS.m.z: a numeric vector

- Charge: a numeric vector

- m.z: a numeric vector

- Mass: a numeric vector

- Resolution: a numeric vector

- Uncalibrated...Calibrated.m.z..ppm.: a numeric vector

- Uncalibrated...Calibrated.m.z..Da.: a numeric vector

- Mass.error..ppm.: a numeric vector

- Mass.error..Da.: a numeric vector

- Uncalibrated.mass.error..ppm.: a numeric vector

- Uncalibrated.mass.error..Da.: a numeric vector

- Max.intensity.m.z.0: a numeric vector

- Retention.time: a numeric vector

- Retention.length: a numeric vector

- Calibrated.retention.time: a numeric vector

- Calibrated.retention.time.start: a numeric vector

- Calibrated.retention.time.finish: a numeric vector

- Retention.time.calibration: a numeric vector

- Match.time.difference: a logical vector

- Match.m.z.difference: a logical vector

- Match.q.value: a logical vector

- Match.score: a logical vector

- Number.of.data.points: a numeric vector

- Number.of.scans: a numeric vector

- Number.of.isotopic.peaks: a numeric vector

- PIF: a numeric vector

- Fraction.of.total.spectrum: a numeric vector

- Base.peak.fraction: a numeric vector

- PEP: a numeric vector

- MS.MS.count: a numeric vector

- MS.MS.scan.number: a numeric vector

- Score: a numeric vector

- Delta.score: a numeric vector

- Combinatorics: a numeric vector

- Intensity: a numeric vector

- Reporter.intensity.corrected.0: a numeric vector

- Reporter.intensity.corrected.1: a numeric vector

- Reporter.intensity.corrected.2: a numeric vector

- Reporter.intensity.corrected.3: a numeric vector

- Reporter.intensity.corrected.4: a numeric vector

- Reporter.intensity.corrected.5: a numeric vector

- Reporter.intensity.corrected.6: a numeric vector

- Reporter.intensity.corrected.7: a numeric vector

- Reporter.intensity.corrected.8: a numeric vector

- Reporter.intensity.corrected.9: a numeric vector

- Reporter.intensity.corrected.10: a numeric vector

- RI1: a numeric vector

- RI2: a numeric vector

- RI3: a numeric vector

- RI4: a numeric vector

- RI5: a numeric vector

- RI6: a numeric vector

- RI7: a numeric vector

- RI8: a numeric vector

- RI9: a numeric vector

- RI10: a numeric vector

- RI11: a numeric vector

- Reporter.intensity.count.0: a numeric vector

- Reporter.intensity.count.1: a numeric vector

- Reporter.intensity.count.2: a numeric vector

- Reporter.intensity.count.3: a numeric vector

- Reporter.intensity.count.4: a numeric vector

- Reporter.intensity.count.5: a numeric vector

- Reporter.intensity.count.6: a numeric vector

- Reporter.intensity.count.7: a numeric vector

- Reporter.intensity.count.8: a numeric vector

- Reporter.intensity.count.9: a numeric vector

- Reporter.intensity.count.10: a numeric vector

- Reporter.PIF: a logical vector

- Reporter.fraction: a logical vector

- Reverse: a character vector

- Potential.contaminant: a logical vector

- id: a numeric vector

- Protein.group.IDs: a character vector

- Peptide.ID: a numeric vector

- Mod..peptide.ID: a numeric vector

- MS.MS.IDs: a character vector

- Best.MS.MS: a numeric vector

- AIF.MS.MS.IDs: a logical vector

- Deamidation..N..site.IDs: a numeric vector

- Oxidation..M..site.IDs: a logical vector

- remove: a logical vector

- dart_PEP: a numeric vector

- dart_qval: a numeric vector

- razor_protein_fdr: a numeric vector

- Deamidation..NQ..Probabilities: a logical vector

- Deamidation..NQ..Score.Diffs: a logical vector

- Deamidation..NQ.: a logical vector

- Reporter.intensity.corrected.11: a logical vector

- Reporter.intensity.corrected.12: a logical vector

- Reporter.intensity.corrected.13: a logical vector

- Reporter.intensity.corrected.14: a logical vector

- Reporter.intensity.corrected.15: a logical vector

- Reporter.intensity.corrected.16: a logical vector

- RI12: a logical vector

- RI13: a logical vector

- RI14: a logical vector

- RI15: a logical vector

- RI16: a logical vector

- Reporter.intensity.count.11: a logical vector

- Reporter.intensity.count.12: a logical vector

- Reporter.intensity.count.13: a logical vector

- Reporter.intensity.count.14: a logical vector

- Reporter.intensity.count.15: a logical vector

- Reporter.intensity.count.16: a logical vector

- Deamidation..NQ..site.IDs: a logical vector

- input_id: a logical vector

- rt_minus: a logical vector

- rt_plus: a logical vector

- mu: a logical vector

- muij: a logical vector

- sigmaij: a logical vector

- pep_new: a logical vector

- exp_id: a logical vector

- peptide_id: a logical vector

- stan_peptide_id: a logical vector

- exclude: a logical vector

- residual: a logical vector

- participated: a logical vector

- peptide: a character vector

### Usage

    data("mqScpData")

### Format

An object of class `data.frame` with 1361 rows and 149 columns.

### Details

The dataset is a subset of the SCoPE2 dataset (version 2, Specht et al. 2019, BioRXiv). The input file `evidence_unfiltered.csv` was downloaded from a Google Drive repository. The MaxQuant evidence file was loaded and the data was cleaned (renaming columns, removing duplicate fields,...). MS runs that were selected in the `scp1` dataset (see `?scp1`) were kept along with a blank run. The data is stored as a `data.frame`.

### See Also

`readSCP()` for an example on how `mqScpData` is parsed into a QFeatures object.

[Package scp version 1.4.0 Index]